MeDiChI 0.4.1 – Model-Based ChIP-chip Deconvolution Algorithm

MeDiChI 0.4.1

:: DESCRIPTION

MeDiChI is method for the automated, model-based deconvolution of protein-DNA binding (Chromatin immunoprecipitation followed by hybridization to a genomic tiling microarray — ChIP-chip) data that discovers DNA binding sites at high resolution (higher resolution than that of the tiling array itself).

::DEVELOPER

Baliga Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R package

:: DOWNLOAD

 MeDiChI

:: MORE INFORMATION

Citation

Bioinformatics. 2008 Feb 1;24(3):396-403. Epub 2007 Dec 1.
Model-based deconvolution of genome-wide DNA binding.
Reiss DJ, Facciotti MT, Baliga NS.

PERT 1.0 – Expression Deconvolution under Varied Environmental Conditions

PERT 1.0

:: DESCRIPTION

The PERT algorithm is designed for expression deconvolution of samples of mixed cell types, where the expression profiles of most of the individual cell types are available and we simply want to estimate the proportion of each mixed sample that is attributable to each individual cell type.

::DEVELOPER

QUON-TITATIVE BIOLOGY LAB

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /
  • Octave

:: DOWNLOAD

 PERT 

:: MORE INFORMATION

Citation

PLoS Comput Biol. 2012;8(12):e1002838. doi: 10.1371/journal.pcbi.1002838. Epub 2012 Dec 20.
PERT: a method for expression deconvolution of human blood samples from varied microenvironmental and developmental conditions.
Qiao W1, Quon G, Csaszar E, Yu M, Morris Q, Zandstra PW.

ISOpure 1.0 / ISOpureR 1.0.18 – Gene Expression Deconvolution and Purification

ISOpure 1.0 / ISOpureR 1.0.18

:: DESCRIPTION

ISOpure uses a set of tumor expression profiles and a panel of healthy tissue expression profiles to generate a purified cancer profile for each tumor sample, and an estimate of the proportion of RNA originating from cancerous cells.

ISOpureR: Deconvolution of Tumour Profiles

::DEVELOPER

QUON-TITATIVE BIOLOGY LABthe Boutros Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • MatLab / R

:: DOWNLOAD

 ISOpure , ISOpureR

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2015 May 14;16:156. doi: 10.1186/s12859-015-0597-x.
ISOpureR: an R implementation of a computational purification algorithm of mixed tumour profiles.
Anghel CV, Quon G, Haider S, Nguyen F, Deshwar AG, Morris QD, Boutros PC

Genome Med. 2013 Mar 28;5(3):29.
Computational purification of individual tumor gene expression profiles leads to significant improvements in prognostic prediction.
Quon G, Haider S, Deshwar AG, Cui A, Boutros PC, Morris Q.

UNDO 1.10.0 – Unsupervised Deconvolution of Tumor-Stromal Mixed Expressions

UNDO 1.10.0

:: DESCRIPTION

UNDO (UNsupervised DecOnvolution) is an R package that can be used to automatically detect cell-specific marker genes located on the scatter radii of mixed gene expressions, estimate cellular proportions in each sample, and deconvolute mixed expressions into cell-specific expression profiles.

::DEVELOPER

Computational Bioinformatics & Bio-imaging Laboratory (CBIL)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • R
  • Bioconductor

:: DOWNLOAD

 UNDO

:: MORE INFORMATION

Citation

UNDO: a Bioconductor R package for unsupervised deconvolution of mixed gene expressions in tumor samples.
Wang N, Gong T, Clarke R, Chen L, Shih IM, Zhang Z, Levine DA, Xuan J, Wang Y.
Bioinformatics. 2015 Jan 1;31(1):137-9. doi: 10.1093/bioinformatics/btu607.

HiTSelect 20140708 – High-throughput Genome Wide Screen Deconvolution Software

HiTSelect 20140708

:: DESCRIPTION

HiTSelect is a software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. HiTSelect provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.

::DEVELOPER

Diaz Lab , Jun S. Song’s Research Group

:: SCREENSHOTS

HiTSelect

:: REQUIREMENTS

  • Windows /Linux/ MacOsX

:: DOWNLOAD

 HiTSelect

:: MORE INFORMATION

Citation

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.
Diaz AA, Qin H, Ramalho-Santos M, Song JS.
Nucleic Acids Res. 2014 Nov 26. pii: gku1197.

MS-Deconv 0.8.0.7370 – Deconvolution of Top-down Spectra

MS-Deconv 0.8.0.7370

:: DESCRIPTION

MS-Deconv is a combinatorial algorithm for spectral deconvolution. The algorithm first generates a large set of candidate isotopomer envelopes for a spectrum, then represents the spectrum as a graph, and finally selects its highest scoring subset of envelopes as a heaviest path in the graph.

::DEVELOPER

CCMS The Center for Computational Mass Spectrometry

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/ MacOsX
  • Java

:: DOWNLOAD

 MS-Deconv 

:: MORE INFORMATION

Citation

Mol Cell Proteomics. 2010 Dec;9(12):2772-82. doi: 10.1074/mcp.M110.002766. Epub 2010 Sep 20.
Deconvolution and database search of complex tandem mass spectra of intact proteins: a combinatorial approach.
Liu X1, Inbar Y, Dorrestein PC, Wynne C, Edwards N, Souda P, Whitelegge JP, Bafna V, Pevzner PA.

CellMix 1.6.2 – Gene Expression Deconvolution

CellMix 1.6.2

:: DESCRIPTION

CellMix , an R package that incorporates most state-of-the-art deconvolution methods, into an intuitive and extendible framework, providing a single entry point to explore, assess and disentangle gene expression data from heterogeneous samples.

::DEVELOPER

The UCT Computational Biology Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX/ Windows
  • R package

:: DOWNLOAD

 CellMix

:: MORE INFORMATION

Citation

Bioinformatics. 2013 Sep 1;29(17):2211-2. doi: 10.1093/bioinformatics/btt351. Epub 2013 Jul 3.
CellMix: a comprehensive toolbox for gene expression deconvolution.
Gaujoux R1, Seoighe C.

MetaboliteDetector 2.5 – Deconvolution and Analysis of GC/MS Data

MetaboliteDetector 2.5

:: DESCRIPTION

Metabolite Detector is a QT4 based software package for the analysis of GC-MS based metabolomics data. The software is especially intended for the analysis of high resoluted GC-MS chromatograms which accumulate during high throughput based metabolmics experiments.

::DEVELOPER

MetaboliteDetector Team

:: SCREENSHOTS

MetaboliteDetector

:: REQUIREMENTS

  • Linux/ Windows 

:: DOWNLOAD

 MetaboliteDetector

:: MORE INFORMATION

Citation

Anal Chem. 2009 May 1;81(9):3429-39. doi: 10.1021/ac802689c.
MetaboliteDetector: comprehensive analysis tool for targeted and nontargeted GC/MS based metabolome analysis.
Hiller K, Hangebrauk J, J?ger C, Spura J, Schreiber K, Schomburg D.

BlindCall 1.0 – Ultra-fast Base-calling of Second-generation Sequencing data by Blind Deconvolution

BlindCall 1.0

:: DESCRIPTION

BlindCall is a simple and ultra-fast non-probabilistic base-calling method for Illumina high-throughput sequencing data based on blind deconvolution.

::DEVELOPER

Héctor Corrada Bravo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 BlindCall

:: MORE INFORMATION

Citation:

Bioinformatics. 2014 May 1;30(9):1214-9. doi: 10.1093/bioinformatics/btu010. Epub 2014 Jan 9.
BlindCall: ultra-fast base-calling of high-throughput sequencing data by blind deconvolution.
Ye C1, Hsiao C, Corrada Bravo H.

PCAdmix 1.0 – Local Ancestry Deconvolution

PCAdmix 1.0

:: DESCRIPTION

PCAdmix is a method that estimates local ancestry via principal components analysis (PCA) using phased haplotypes.  The method considers data chromosome by chromosome.

:: DEVELOPER

the Bustamante Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

  PCAdmix

:: MORE INFORMATION

Citation

Hum Biol. 2012 Aug;84(4):343-64. doi: 10.3378/027.084.0401.
PCAdmix: principal components-based assignment of ancestry along each chromosome in individuals with admixed ancestry from two or more populations.
Brisbin A1, Bryc K, Byrnes J, Zakharia F, Omberg L, Degenhardt J, Reynolds A, Ostrer H, Mezey JG, Bustamante CD.